Questions tagged [genetics]

The scientific study of the principles of heredity and the variation of inherited traits among related organisms.

Genetics is the study of genes — what they are, what they do, and how they work. Genes inside the nucleus of a cell are strung together in such a way that the sequence carries information: that information determines how living organisms inherit various features (phenotypic traits). For example, offspring produced by sexual reproduction usually look similar to each of their parents because they have inherited some of each of their parents' genes. Genetics identifies which features are inherited, and explains how these features pass from generation to generation. In addition to inheritance, genetics studies how genes are turned on and off to control what substances are made in a cell-gene expression.

Nowadays, the genetics is interesting in computer science too. It can propose own advances and results of the investigations to describe the information interpretation for very complex objects and needed methods on the algorithmic level. For example, one gene can save value about one feature of the object, furthermore, using different methods of information coding we can expand properties of one gene whereby different shades. Also, considering gene on the abstract level of our understanding, we can build a very powerful system of equations which will be describing the object completely from different aspects.

To know more.

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Merge by Range in R - Applying Loops

I posted a question here: Matched Range Merge in R about merging two files based on a number in one file falling into a range in the second file. Thus far, I have been unsuccessful in piecing together code to accomplish this. The issue I am having…
mfk534
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Syntaxless programming language

This is probably a very strange question, and it definitely is. I'm not too familiar on how programming languages are made with conventional methods, so I'm wondering, is it possible to design a syntaxless programming language? This means that any…
Pwnna
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Converting nucleotides to amino acids using JavaScript

I'm creating a Chrome Extension that converts a string of nucleotides of length nlen into the corresponding amino acids. I've done something similar to this before in Python but as I'm still very new to JavaScript I'm struggling to translate that…
happy
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Convert data frame of snp genotypes in numeric matrix

snp1 <- c("AA", "AT", "AA", "TT", "AA", "AT", "AA", "AA", "AA", "AT") snp2 <- c("GG", "GC", "GG", "CC", "CC", "GC", "GG", "GG", "GG", "GC") df1 <- data.frame(snp1, snp2) num1 <- c(1, 2, 1, 3, 1, 2, 1, 1, 1, 2) num2 <- c(1, 2, 1, 3, 3, 2, 1, 1, 1,…
milan
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Warning message clarification

I'm using SNPassoc R package for finding association between data SNPs and a continuous variable outcome. I run the analysis and I got the results; however, I got warning message which is: Warning in terms.formula(formula, data = data) : 'varlist'…
Marwah Al-kaabi
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Convert space separated text file into named vectors to calculate HWE

I'm dealing with text files and vectors. I have a space separated text file with the following format: id1 AA 44 AG 20 GG 36 id2 CC 30 CT 22 TT 48 id3 CT 60 CC 30 TT 10 ... And I need a code that loops through each line and put the id in a variable…
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Writing a GUI for the BRCAPRO Cancer Gene Risk Calculation Engine

I think this is a completely unique question on Stack Overflow. First some background: I've been asked to write a new GUI on top of a calculation engine called BRCAPRO (brack-a-pro). BRCAPRO implements a Mendelian computational model based on a…
Kyle Noland
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How to iterate through independent variables, performing multiple linear regressions using the tidyverse framework?

My data: library(tidyverse) library(lme4) myData <- structure(list(Subjects = c(4L, 3L, 5L, 1L, 9L, 6L, 10L, 2L, 8L, 7L), Gene1 = c(0.318630087617032, -0.58179068471591, 0.714532710891568, -0.825259425862769, -0.359862131395465,…
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Order dataframe by colnames

I have a dataframe like this : G2_ref G10_ref G12_ref G2_alt G10_alt G12_alt 20011953 3 6 0 5 1 5 12677336 0 0 0 1 3 6 20076754 0 3 0 12 16 8…
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How to compare 2 lists of ranges in bash?

Using bash script (Ubuntu 16.04), I'm trying to compare 2 lists of ranges: does any number in any of the ranges in file1 coincide with any number in any of the ranges in file2? If so, print the row in the second file. Here I have each range as 2…
Marla
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How to apply test functions to genetic algorithm

I have written following code for population evolution (Genetic Algorithm Implementation): Individual.java import java.util.Random; public class Individual { public static int SIZE = 500; private int[] genes = new int[SIZE]; private…
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find and delete rows which have greater than 5% missing data

I have a matrix (called results) that looks like this id1 id2 id3 id4 id5 id6 id7 id8 id9 snp1 1 2 0 NA 1 1 1 2 1 snp2 2 2 2 2 0 2 NA NA 0 snp3 NA NA 1 NA 0 NA NA 2 2 So far, I have deleted rows and…
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Gene ontology (GO) analysis for a list of Genes (with ENTREZID) in R?

I am very new with the GO analysis and I am a bit confuse how to do it my list of genes. I have a list of genes (n=10): gene_list SYMBOL ENTREZID GENENAME 1 AFAP1 60312 actin filament associated protein 1 2 …
user3576287
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R- How to plot correct pie charts in haploNet haplotyp Networks {pegas} {ape} {adegenet}

When using the haploNet package to make some plots on a haplotype network, I used a script available on the internet to do so. However I think there is something wrong. The script is available in form of the woodmouse example. The code I used is: x…
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How to plot Pie charts in haploNet Haplotype Networks {pegas}

I'm trying to use haploNet function of {pegas} to plot a haplotype network, but i`m having trouble putting equal haplotypes from different populations in a same piechart. I can build a haplotype net with the following script: x <-…
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